A laser system is calibrated with a tomography system capable of measuring locations of structure within an optically transmissive material such as a tissue of an eye. Alternatively or in combination, the tomography system can be used to track the location of the eye and adjust the treatment in response to one or more of the location or an orientation of the eye. In many embodiments, in situ calibration and tracking of an optically transmissive tissue structure such as an eye can be provided. The optically transmissive material may comprise one or more optically transmissive structures of the eye, or a non-ocular optically transmissive material such as a calibration gel in a container or an optically transmissive material of a machined part.